diff --git a/README.md b/README.md
index 9d2f2b0716..8f7b997ff4 100644
--- a/README.md
+++ b/README.md
@@ -188,7 +188,6 @@ kandev/
 │   │   └── Makefile
 │   └── web/                  # Frontend application
 ├── docs/                     # Architecture and planning docs
-├── migrations/               # Database migrations (future)
 ├── deployments/              # Deployment configs
 └── scripts/                  # Utility scripts (including e2e-test.sh)
 ```
diff --git a/apps/backend/internal/agent/settings/store/sqlite.go b/apps/backend/internal/agent/settings/store/sqlite.go
index 4894b465de..5f9064f1ba 100644
--- a/apps/backend/internal/agent/settings/store/sqlite.go
+++ b/apps/backend/internal/agent/settings/store/sqlite.go
@@ -58,6 +58,7 @@ func (r *sqliteRepository) initSchema() error {
 		auto_approve INTEGER NOT NULL DEFAULT 0,
 		dangerously_skip_permissions INTEGER NOT NULL DEFAULT 0,
 		allow_indexing INTEGER NOT NULL DEFAULT 1,
+		cli_passthrough INTEGER NOT NULL DEFAULT 0,
 		plan TEXT DEFAULT '',
 		created_at DATETIME NOT NULL,
 		updated_at DATETIME NOT NULL,
@@ -80,19 +81,7 @@ func (r *sqliteRepository) initSchema() error {
 	CREATE INDEX IF NOT EXISTS idx_agent_profiles_agent_id ON agent_profiles(agent_id);
 	`
 	_, err := r.db.Exec(schema)
-	if err != nil {
-		return err
-	}
-	if err := sqlite.EnsureColumn(r.db, "agent_profiles", "deleted_at", "DATETIME"); err != nil {
-		return err
-	}
-	if err := sqlite.EnsureColumn(r.db, "agent_profiles", "agent_display_name", "TEXT NOT NULL DEFAULT ''"); err != nil {
-		return err
-	}
-	if err := sqlite.EnsureColumn(r.db, "agent_profiles", "cli_passthrough", "INTEGER NOT NULL DEFAULT 0"); err != nil {
-		return err
-	}
-	return nil
+	return err
 }
 
 func (r *sqliteRepository) Close() error {
diff --git a/apps/backend/internal/editors/store/sqlite.go b/apps/backend/internal/editors/store/sqlite.go
index 1d783ada26..d8415b4431 100644
--- a/apps/backend/internal/editors/store/sqlite.go
+++ b/apps/backend/internal/editors/store/sqlite.go
@@ -72,21 +72,7 @@ func (r *sqliteRepository) initSchema() error {
 	);
 	`
 	_, err := r.db.Exec(schema)
-	if err != nil {
-		return err
-	}
-	columns := []columnDef{
-		{name: "name", typ: "TEXT", defaultValue: "''"},
-		{name: "kind", typ: "TEXT", defaultValue: "'built_in'"},
-		{name: "config", typ: "TEXT", defaultValue: "NULL"},
-		{name: "installed", typ: "INTEGER", defaultValue: "0"},
-	}
-	for _, column := range columns {
-		if err := ensureColumn(r.db, "editors", column); err != nil {
-			return err
-		}
-	}
-	return nil
+	return err
 }
 
 func (r *sqliteRepository) ensureDefaults(ctx context.Context) error {
@@ -319,47 +305,6 @@ func scanEditor(scanner interface{ Scan(dest ...any) error }) (*models.Editor, e
 	return editor, nil
 }
 
-type columnDef struct {
-	name         string
-	typ          string
-	defaultValue string
-}
-
-func ensureColumn(db *sql.DB, table string, column columnDef) error {
-	rows, err := db.Query(fmt.Sprintf("PRAGMA table_info(%s)", table))
-	if err != nil {
-		return err
-	}
-	defer func() {
-		_ = rows.Close()
-	}()
-	for rows.Next() {
-		var (
-			cid        int
-			name       string
-			typ        string
-			notNull    int
-			defaultVal sql.NullString
-			pk         int
-		)
-		if err := rows.Scan(&cid, &name, &typ, &notNull, &defaultVal, &pk); err != nil {
-			return err
-		}
-		if name == column.name {
-			return nil
-		}
-	}
-	alter := fmt.Sprintf(
-		"ALTER TABLE %s ADD COLUMN %s %s DEFAULT %s",
-		table,
-		column.name,
-		column.typ,
-		column.defaultValue,
-	)
-	_, err = db.Exec(alter)
-	return err
-}
-
 func marshalConfig(config json.RawMessage) (string, error) {
 	if len(config) == 0 {
 		return "", nil
diff --git a/apps/backend/internal/task/repository/sqlite/base.go b/apps/backend/internal/task/repository/sqlite/base.go
index 823bf63271..31ec960ba2 100644
--- a/apps/backend/internal/task/repository/sqlite/base.go
+++ b/apps/backend/internal/task/repository/sqlite/base.go
@@ -4,8 +4,6 @@ package sqlite
 import (
 	"database/sql"
 	"fmt"
-
-	commonsqlite "github.com/kandev/kandev/internal/common/sqlite"
 )
 
 // Repository provides SQLite-based task storage operations.
@@ -45,11 +43,6 @@ func (r *Repository) DB() *sql.DB {
 	return r.db
 }
 
-// ensureColumn adds a column to a table if it doesn't exist
-func (r *Repository) ensureColumn(table, column, definition string) error {
-	return commonsqlite.EnsureColumn(r.db, table, column, definition)
-}
-
 // ensureWorkspaceIndexes creates workspace-related indexes
 func (r *Repository) ensureWorkspaceIndexes() error {
 	if _, err := r.db.Exec(`CREATE INDEX IF NOT EXISTS idx_tasks_workspace_id ON tasks(workspace_id)`); err != nil {
@@ -129,6 +122,7 @@ func (r *Repository) initSchema() error {
 	CREATE TABLE IF NOT EXISTS boards (
 		id TEXT PRIMARY KEY,
 		workspace_id TEXT NOT NULL DEFAULT '',
+		workflow_template_id TEXT DEFAULT '',
 		name TEXT NOT NULL,
 		description TEXT DEFAULT '',
 		created_at DATETIME NOT NULL,
@@ -372,88 +366,6 @@ func (r *Repository) initSchema() error {
 		return err
 	}
 
-	// Ensure columns exist for schema migrations
-	if err := r.ensureColumn("boards", "workspace_id", "TEXT NOT NULL DEFAULT ''"); err != nil {
-		return err
-	}
-	if err := r.ensureColumn("boards", "workflow_template_id", "TEXT DEFAULT ''"); err != nil {
-		return err
-	}
-	if err := r.ensureColumn("tasks", "workspace_id", "TEXT NOT NULL DEFAULT ''"); err != nil {
-		return err
-	}
-	if err := r.ensureColumn("workspaces", "default_executor_id", "TEXT DEFAULT ''"); err != nil {
-		return err
-	}
-	if err := r.ensureColumn("workspaces", "default_environment_id", "TEXT DEFAULT ''"); err != nil {
-		return err
-	}
-	if err := r.ensureColumn("workspaces", "default_agent_profile_id", "TEXT DEFAULT ''"); err != nil {
-		return err
-	}
-
-	if err := r.ensureColumn("environments", "is_system", "INTEGER NOT NULL DEFAULT 0"); err != nil {
-		return err
-	}
-	if err := r.ensureColumn("repositories", "deleted_at", "DATETIME"); err != nil {
-		return err
-	}
-	if err := r.ensureColumn("repositories", "worktree_branch_prefix", "TEXT DEFAULT 'feature/'"); err != nil {
-		return err
-	}
-	if err := r.ensureColumn("repositories", "pull_before_worktree", "INTEGER NOT NULL DEFAULT 1"); err != nil {
-		return err
-	}
-	if err := r.ensureColumn("repositories", "dev_script", "TEXT DEFAULT ''"); err != nil {
-		return err
-	}
-	if err := r.ensureColumn("executors", "deleted_at", "DATETIME"); err != nil {
-		return err
-	}
-	if err := r.ensureColumn("executors", "resumable", "INTEGER NOT NULL DEFAULT 1"); err != nil {
-		return err
-	}
-	if err := r.ensureColumn("environments", "deleted_at", "DATETIME"); err != nil {
-		return err
-	}
-
-	// Ensure new message columns exist for existing databases
-	if err := r.ensureColumn("task_session_messages", "type", "TEXT NOT NULL DEFAULT 'message'"); err != nil {
-		return err
-	}
-	if err := r.ensureColumn("task_session_messages", "metadata", "TEXT DEFAULT '{}'"); err != nil {
-		return err
-	}
-	if err := r.ensureColumn("task_session_messages", "task_session_id", "TEXT NOT NULL DEFAULT ''"); err != nil {
-		return err
-	}
-	if err := r.ensureColumn("task_session_messages", "turn_id", "TEXT DEFAULT ''"); err != nil {
-		return err
-	}
-
-	// Ensure container_id column exists for existing databases
-	if err := r.ensureColumn("task_sessions", "container_id", "TEXT NOT NULL DEFAULT ''"); err != nil {
-		return err
-	}
-	if err := r.ensureColumn("task_sessions", "executor_id", "TEXT DEFAULT ''"); err != nil {
-		return err
-	}
-	if err := r.ensureColumn("task_sessions", "environment_id", "TEXT DEFAULT ''"); err != nil {
-		return err
-	}
-	if err := r.ensureColumn("task_sessions", "state", "TEXT NOT NULL DEFAULT 'CREATED'"); err != nil {
-		return err
-	}
-	if err := r.ensureColumn("task_sessions", "is_primary", "INTEGER DEFAULT 0"); err != nil {
-		return err
-	}
-	if err := r.ensureColumn("task_sessions", "workflow_step_id", "TEXT DEFAULT ''"); err != nil {
-		return err
-	}
-	if err := r.ensureColumn("task_sessions", "review_status", "TEXT DEFAULT ''"); err != nil {
-		return err
-	}
-
 	if err := r.ensureDefaultWorkspace(); err != nil {
 		return err
 	}
diff --git a/apps/backend/internal/user/store/sqlite.go b/apps/backend/internal/user/store/sqlite.go
index 53cba4d2cd..aa3f943a7c 100644
--- a/apps/backend/internal/user/store/sqlite.go
+++ b/apps/backend/internal/user/store/sqlite.go
@@ -7,7 +7,6 @@ import (
 	"fmt"
 	"time"
 
-	"github.com/kandev/kandev/internal/common/sqlite"
 	"github.com/kandev/kandev/internal/user/models"
 )
 
@@ -53,17 +52,10 @@ func (r *sqliteRepository) initSchema() error {
 	if _, err := r.db.Exec(schema); err != nil {
 		return err
 	}
-	if err := r.ensureUserSettingsColumn(); err != nil {
-		return err
-	}
 
 	return r.ensureDefaultUser()
 }
 
-func (r *sqliteRepository) ensureUserSettingsColumn() error {
-	return sqlite.EnsureColumn(r.db, "users", "settings", "TEXT NOT NULL DEFAULT '{}'")
-}
-
 func (r *sqliteRepository) ensureDefaultUser() error {
 	ctx := context.Background()
 	var count int
diff --git a/apps/backend/internal/workflow/repository/sqlite.go b/apps/backend/internal/workflow/repository/sqlite.go
index b2a03a7704..d1e3d041b0 100644
--- a/apps/backend/internal/workflow/repository/sqlite.go
+++ b/apps/backend/internal/workflow/repository/sqlite.go
@@ -33,11 +33,6 @@ func (r *Repository) DB() *sql.DB {
 	return r.db
 }
 
-// ensureColumn adds a column to a table if it doesn't exist.
-func (r *Repository) ensureColumn(table, column, definition string) error {
-	return sqlite.EnsureColumn(r.db, table, column, definition)
-}
-
 // initSchema creates the database tables if they don't exist.
 func (r *Repository) initSchema() error {
 	// Create workflow_templates table
@@ -102,11 +97,6 @@ func (r *Repository) initSchema() error {
 		return fmt.Errorf("failed to create session_step_history table: %w", err)
 	}
 
-	// Run migrations for existing tables
-	if err := r.runMigrations(); err != nil {
-		return fmt.Errorf("failed to run migrations: %w", err)
-	}
-
 	// Seed system templates
 	if err := r.seedSystemTemplates(); err != nil {
 		return fmt.Errorf("failed to seed system templates: %w", err)
@@ -120,27 +110,6 @@ func (r *Repository) initSchema() error {
 	return nil
 }
 
-// runMigrations adds columns to existing tables.
-func (r *Repository) runMigrations() error {
-	// Add workflow_template_id to boards table
-	if err := r.ensureColumn("boards", "workflow_template_id", "TEXT"); err != nil {
-		return fmt.Errorf("failed to add workflow_template_id to boards: %w", err)
-	}
-
-	// Add workflow-related columns to task_sessions table
-	if err := r.ensureColumn("task_sessions", "is_primary", "INTEGER DEFAULT 0"); err != nil {
-		return fmt.Errorf("failed to add is_primary to task_sessions: %w", err)
-	}
-	if err := r.ensureColumn("task_sessions", "workflow_step_id", "TEXT"); err != nil {
-		return fmt.Errorf("failed to add workflow_step_id to task_sessions: %w", err)
-	}
-	if err := r.ensureColumn("task_sessions", "review_status", "TEXT"); err != nil {
-		return fmt.Errorf("failed to add review_status to task_sessions: %w", err)
-	}
-
-	return nil
-}
-
 // seedDefaultWorkflowSteps creates default workflow steps for boards that don't have any.
 // Uses the simple template as the default workflow.
 func (r *Repository) seedDefaultWorkflowSteps() error {